Sequence
atgc intronic sequence ATGC exonic sequence...gagtagacaccgacactgagtagattcatgattttgaaacgtcatcaatctaatgtaacgattgctcaagtcttaactacttgacttacaatgtgtgtagGTTTATCATCCAAATATAGATCTGGAAGGCAATGTGTGTCTGAATATTCTTCGTGAGGATTGGAAGCCTGTGCTGAGTGTAAACTCTATCATATATGGTC
Basic information
species | Physcomitrella patens |
transcript | PP1S61_126V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S61_126V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os10g11260.2 (Oryza sativa), 3'ss of exon 4
gagtagacaccgacactgag---tagattcatgattttgaaacgtca--tcaatctaatgtaacgattgctcaagtcttaactact-tgacttacaa--tgtgtgtagGTTTATCATCCAAATATAGATCTGGAAGGCAATGTGTGTCTGAATATTCTTCGTGAGGATTGGAAGCCTGTGCTGAGTGTAAACTCTATCATATATGGTC
|| | | | || || || | | ||| | | | | | | || | |||| || | || || ||| || || | |||| || ||||||||||| ||| ||||||| ||||| || ||||| ||| | ||||| |||||||||||||| || | | ||| || | || ||||| |
--gtgaagtgcaagaccaaggtataagatggggctttctatgctatatattttcccagtgaatatgttgcctcttaaccaatttctatgcattataacttgcattcagGTATACCATCCAAATATTGATTTGGAAGGAAATGTATGCCTGAACATTTTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACTGTTATTTATGGCC
upper sequence: PP1S61_126V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os10g11260.3 (Oryza sativa), 3'ss of exon 4
gagtagacaccgacactgagtagattcatgattttgaaacgtcatcaatctaatgtaacgattgctcaagtcttaactact-tgacttacaatgtgtgtagGTTTATCATCCAAATATAGATCTGGAAGGCAATGTGTGTCTGAATATTCTTCGTGAGGATTGGAAGCCTGTGCTGAGTGTAAACTCTATCATATATGGTC
||| | | || || | ||||| | | ||| | || | || ||| | || | | | |||| || | |||| || ||||||||||| ||| ||||||| ||||| || ||||| ||| | ||||| |||||||||||||| || | | ||| || | || ||||| |
--gtataagatggggctttctatgctatatatttt----cccagtgaatatgttgcctc--ttaaccaatttctatgcattataacttgcatt-----cagGTATACCATCCAAATATTGATTTGGAAGGAAATGTATGCCTGAACATTTTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACTGTTATTTATGGCC
upper sequence: PP1S61_126V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G115939_T02 (Zea mays), 3'ss of exon 5
gagtagacaccgacactgagtagattcatgattttgaaacgtcatcaatctaatgtaacgattgctcaagtc-ttaactacttgact--tacaa---tgtgtgtagGTTTATCATCCAAATATAGATCTGGAAGGCAATGTGTGTCTGAATATTCTTCGTGAGGATTGGAAGCCTGTGCTGAGTGTAAACTCTATCATATATGGTC-----------------
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--gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcaggtgtaccatccaaatattgatttggaaGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCCTGAATCTTCTTTTTACG
upper sequence: PP1S61_126V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G115939_T04 (Zea mays), 3'ss of exon 4
gagtagacaccgacactgagtagattcatgattttgaaacgtcatcaatctaatgtaacgattgctcaagtc-ttaactacttgact--tacaa---tgtgtgtagGTTTATCATCCAAATATAGATCTGGAAGGCAATGTGTGTCTGAATATTCTTCGTGAGGATTGGAAGCCTGTGCTGAGTGTAAACTCTATCATATATGGTC
||| | | | | || || ||| || | | ||| | ||| | | || |||| |||| ||||| || || || || | |||| || ||||||||||| ||| ||||||||||||| |||||||| ||||| ||||| |||||||||||||| || | | ||| | | || ||||| |
--gtataaggcagtattctttacatctatggttctttctgattatccactaaattacatttcttctaaagtgattaaatacttagctgttataaacatgcattcagGTGTACCATCCAAATATTGATTTGGAAGGCAATGTCTGTCTGAACATTCTGCGTGAAGATTGGAAGCCTGTTCTCAACATCAACACCGTTATTTATGGCC
upper sequence: PP1S61_126V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G102421_T01 (Zea mays), 3'ss of exon 6
gagtagacaccgacactgagtagattcatgattttgaaacgtcatcaatctaatgtaacgattgctcaagtcttaa----ctacttgacttacaatgtgtgt---agGTTTATCATCCAAATATAGATCTGGAAGGCAATGTGTGTCTGAATATTCTTCGTGAGGATTGGAAGCCTGTGCTGAGTGTAAACTCTATCATATATGGTC
||| | | | || || ||| || | | | || | ||| | | || ||| ||| | | || || | |||| || ||||||||||| ||||||||||||||||| |||||||| ||||| || || |||||||||||||| || | | ||| || | || ||||| |
--gtataagacagtatcctttacatctatggttctttctcattctccactaaattgcatttcctatgaaacgataaaatactatgttgttataaacatgcatttcagGTGTACCATCCAAATATTGATCTGGAAGGCAATGTCTGTCTGAACATTCTGCGCGAAGATTGGAAGCCTGTTCTCAACATCAACACTGTTATTTATGGCC
upper sequence: PP1S61_126V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA02G06580.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------gagtagacaccgacactgagtagattcatgattttgaaacgtcatcaatctaatgtaacgattgctcaagtc-ttaacta-cttgacttacaatgtgtgtagGTTTATCATCCAAATATAGATCTGGAAGGCAATGTGTGTCTGAATATTCTTCGTGAGGATTGGAAGCCTGTGCTGAGTGTAAACTCTATCATATATGGTC
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gtaggaactaggagatcttggttatctttggtattattaactcattcttttttatgtacatc-atac-gtgtttaatcttgcttgtgtcatatttgtggtttttccttgtctgtttcaaagtcattaattaatttgtcatgtcatatatgtagGTCTACCATCCAAATATAGACTTGGAAGGAAATGTTTGCCTTAACATCCTACGAGAAGATTGGAAACCTGTCCTCAATATAAACTCTATCATCTACGGCTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|18357195|gb|BJ189254.1|BJ189254EST: TATCGCAGGTGTATCCTCACGAAGCACCAAAGGTCAAATGCAAGACAAAG GTTTATCATCCAAATATAGATCTGGAAGGCAATGTGTGTCTGAATATTCTT
genomic: TATCGCAGGTGTATCCTCACGAAGCACCAAAGGTCAAATGCAAGACAAAGgtaggatgag ... atgtgtgtagGTTTATCATCCAAATATAGATCTGGAAGGCAATGTGTGTCTGAATATTCTT
EST:
gi|37836564|gb|BJ594572.1|BJ594572EST: TATCGCAGGTGTATCCTCACGAAGCACCAAAGGTCAAATGCAAGACAAAG GTTTATCATCCAAATATAGATCTGGAAGGCAATGTGTGTCTGAATATTCTT
genomic: TATCGCAGGTGTATCCTCACGAAGCACCAAAGGTCAAATGCAAGACAAAGgtaggatgag ... atgtgtgtagGTTTATCATCCAAATATAGATCTGGAAGGCAATGTGTGTCTGAATATTCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatctaatgtaacgattgctcaagtcttaactacttgacttacaatgtgtgtagGTTTATCATCCAAATATAGATCTGGAAGGCAATGTGTGTCTGAATATTCTTCGTGAGGATTGGAAGCCTGTGCTGAGTGTAAACTCTATCATATATGGTC
gacttac putative branch site (score: 2)
taatgtaa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gagtagacaccgacactgagtagattcatgattttgaaacgtcatcaatctaatgtaacgattgctcaagtcttaactacttgacttacaatgtgtgtagGTTTATCATCCAAATATAGATCTGGAAGGCAATGTGTGTCTGAATATTCTTCGTGAGGATTGGAAGCCTGTGCTGAGTGTAAACTCTATCATATATGGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG